Variant report

Variant	rs3812471
Chromosome Location	chr8:125498547-125498548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:125498291-125499105	U87	brain:	n/a	n/a
2	EP300	chr8:125498031-125500117	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr8:125497925-125499718	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr8:125498501-125499947	A549	lung:	n/a	n/a
5	POLR2A	chr8:125498153-125500095	GM12878	blood:	n/a	n/a
6	POLR2A	chr8:125498514-125500049	K562	blood:	n/a	n/a
7	POLR2A	chr8:125498213-125499435	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr8:125498407-125499230	PFSK-1	brain:	n/a	n/a
9	GATA3	chr8:125498449-125498568	SH-SY5Y	brain:	n/a	n/a
10	POLR2A	chr8:125498472-125499211	GM12878	blood:	n/a	n/a
11	POLR2A	chr8:125497761-125504238	K562	blood:	n/a	n/a
12	POLR2A	chr8:125498461-125498587	ProgFib	skin:	n/a	n/a
13	POLR2A	chr8:125498026-125499884	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr8:125498453-125499862	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr8:125498494-125498628	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr8:125498293-125499370	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr8:125497917-125498570	U87	brain:	n/a	n/a
18	POLR2A	chr8:125497923-125498560	U87	brain:	n/a	n/a
19	POLR2A	chr8:125498331-125498854	U87	brain:	n/a	n/a
20	MXI1	chr8:125497858-125500460	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr8:125497861-125499332	MCF-7	breast:	n/a	n/a
22	POLR2A	chr8:125498312-125500182	PFSK-1	brain:	n/a	n/a
23	BCL3	chr8:125498479-125499306	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125496558..125498928-chr8:125508129..125510678,4	K562	blood:
2	chr8:125497640..125500390-chr8:125515710..125518211,2	K562	blood:
3	chr8:125497001..125499898-chr8:125500699..125503419,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000253106	TF binding region
ENSG00000253106	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10091243	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10092569	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10106292	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11987932	0.83[EUR][1000 genomes]
rs11991829	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12542293	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12548235	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28725399	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812474	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3812475	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3886003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4128468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4132855	0.92[MEX][hapmap]
rs4269525	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4269526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4870901	0.84[AMR][1000 genomes]
rs4871498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6470243	0.80[EUR][1000 genomes]
rs6470245	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6982197	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6984985	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6987343	0.92[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6993926	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7001480	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7005393	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7007115	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7009290	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7010411	0.90[JPT][hapmap]
rs7013683	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7812331	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7812911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7825599	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827791	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7830506	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv891433	chr8:125438093-125498547	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3812471	TRMT12	cis	multi-tissue	Pritchard
rs3812471	ZHX2	cis	parietal	SCAN
rs3812471	TRMT12	Cis_1M	lymphoblastoid	RTeQTL
rs3812471	TRMT12	cis	Whole Blood	GTEx
rs3812471	TRMT12	cis	uninvolved skin	skin_eQTL
rs3812471	TRMT12	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125488000-125503400	Weak transcription	Spleen	Spleen
2	chr8:125488200-125515800	Weak transcription	Lung	lung
3	chr8:125488200-125550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:125489000-125501800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr8:125489000-125503400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr8:125489000-125505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:125489000-125519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:125489000-125531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:125489000-125541200	Weak transcription	Gastric	stomach
10	chr8:125489000-125543400	Weak transcription	Small Intestine	intestine
11	chr8:125489200-125498600	Weak transcription	A549	lung
12	chr8:125489200-125498600	Weak transcription	HSMMtube	muscle
13	chr8:125489400-125501800	Weak transcription	Fetal Intestine Small	intestine
14	chr8:125489600-125498600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:125493000-125498800	Weak transcription	Pancreas	Pancrea
16	chr8:125493000-125499000	Weak transcription	Psoas Muscle	Psoas
17	chr8:125493000-125499600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:125493200-125539400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr8:125494200-125498600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr8:125496000-125512600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr8:125496400-125498600	Weak transcription	Colonic Mucosa	Colon
22	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr8:125496800-125498800	Weak transcription	NHLF	lung
24	chr8:125496800-125503400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:125496800-125503400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr8:125496800-125513200	Weak transcription	Brain Angular Gyrus	brain
27	chr8:125496800-125521200	Weak transcription	Fetal Heart	heart
28	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr8:125497000-125499200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr8:125497200-125498800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr8:125497200-125498800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr8:125497400-125499200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr8:125497600-125505200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr8:125497800-125500200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr8:125497800-125502400	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr8:125497800-125504000	Strong transcription	Primary B cells from cord blood	blood
37	chr8:125497800-125506200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr8:125498000-125498600	Genic enhancers	Brain Anterior Caudate	brain
39	chr8:125498000-125498600	Genic enhancers	Brain Substantia Nigra	brain
40	chr8:125498000-125498600	Genic enhancers	Fetal Brain Female	brain
41	chr8:125498000-125498600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr8:125498000-125499400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr8:125498000-125499400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr8:125498000-125499600	Strong transcription	Fetal Muscle Leg	muscle
45	chr8:125498000-125499800	Strong transcription	Ovary	ovary
46	chr8:125498000-125499800	Genic enhancers	NHDF-Ad	bronchial
47	chr8:125498000-125500000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr8:125498000-125500000	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr8:125498000-125500000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr8:125498000-125500000	Strong transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links